When install any new package I get errors saying Rtools is not found. I followed the manual install instructions for Rtools but still get the same error message.
> install.packages("phyloseq")
WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding
It seems R is not finding Rtools. Is there anyway to fix this?
I have noticed a second issue of previously installed packages disappearing also when starting new R sessions. Could these two issues be linked?
My R version in 4.0 and I am working in Windows 64bit
After installation is complete, you need to perform one more step to be able to compile R packages: you need to put the location of the Rtools make utilities (bash, make, etc) on the PATH. The easiest way to do so is create a text file .Renviron in your Documents folder which contains the following line:
writeLines('PATH="${RTOOLS40_HOME}\\usr\\bin;${PATH}"', con = "~/.Renviron")
Now restart R, and verify that make can be found, which should show the path to your Rtools installation.
Sys.which("make")
## "C:\\rtools40\\usr\\bin\\make.exe"
https://cran.r-project.org/bin/windows/Rtools/
The second part with packages not being found has to do with upgrading the R version e.g. 3.5 to 3.6 or 3.6 to 4.0. If you go to Documents\R\win-library there will be a version folder with the libraries installed inside. Here is a script that will install the old libraries.
lib_loc <- "C:/Users/apdev/Documents/R/win-library/3.3"
to_install <- unname(installed.packages(lib.loc = lib_loc)[, "Package"])
to_install
install.packages(pkgs = to_install)
https://community.rstudio.com/t/reinstalling-packages-on-new-version-of-r/7670/4
Related
For many R packages I try to install (on my Windows 10 machine), I get a warning:
> install.packages('rstan')
WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:
I thought this was just an erroneous error message since the installation seemed to proceed anyway, but recently I tried to install a package (rstan) and found it completely nonfunctional. My hunch is that since rstan relies completely on compiling code with rcpp, maybe I only got away with the previous packages because I wasn't using the functions in them that relied on Rtools.
I reinstalled Rtools 4.0, and devtools::find_rtools() returns TRUE. But when I run Sys.getenv()['PATH'] there is no Rtools on the path. There isn't a place in the installation process to tell it I want Rtools on the path either, so these instructions don't help - the menus they refer to don't exist for me. So I thought this might be an issue where the new Rtools 4.0 doesn't put itself on the system path. But the problem persisted even after I directly edited the Windows path environment variables (both system and user versions) to include the path given to me by pkgbuild::rtools_path() (C:\rtools40\usr\bin, a path which both exists and appears to be correct).
This doesn't seem to be the same problem as Rtools 4.0 (Rstudio falsely claims it was deleted), since there are no claims Rtools was deleted. It's also not the same as Rtools not being detected by R as far as I can tell: I'm not leaving any features out of my Rtools installation - I'm not even getting the option to in my install wizard.
Would appreciate any advice or recommendations.
Rtools40 requires that you add its bin directory to your PATH variable. The full instructions are here.
You can update your ~/.Renviron file with any of the following methods:
You can do that manually by opening ~/.Renviron and putting the following in it:
PATH="${RTOOLS40_HOME}\usr\bin;${PATH}"
You can also use R (Gui or RStudio or Shell) with the following:
writeLines(
'PATH="${RTOOLS40_HOME}\\usr\\bin;${PATH}"',
con = file("~/.Renviron", open = "a")
)
Both of these methods require a restart of R.
I am trying to install mvpart and MVPARTwrap packages in R version 3.6.1.
I install on my PC the folder of these two packages in zip version and load them in the relative folder of the package.
When I run the script library(mvpart) I get this message:
ERROR: 'mvpart' package was built before R 3.0.0: please reinstall it."
I try to load this library in the old version of R (version 2.15) and the message is
in install.packages (mvpart): object 'mvpart' not found".
I do not understand why it is impossible to load this package. Thanks so much.
Maybe the answer is no more relevant, but I just had to install those libraries so maybe it will still help someone later. I suggest the install from github as it will install dependencies, you need however to be able to compile the source. So here we go :
first install rtools if it is not already installed go here and follow the instruction
update/install devtools if necessary as described here
using this command, it should work now. you may be asked to update some packages, accept all
devtools::install_github("cran/mvpart")
I just installed R3.5 (and RStudio) on a new computer that has not previously had R on it. I then installed the devtools package, and when I went to install a package off of github, I realized (when prompted!) I had forgotten to install Rtools, so I followed the prompts to do so. Interestingly, this R tools installed to the directory of C:\RBuildTools by default and with no prompts for setting path variables as I had recalled in previous versions.
When I reloaded R, I was prompted to install Rtools again. My path contained no reference to Rtools (or the Rbuildtools directory), and remembering that my past installations had used the dir C:\Rtools, I decided to uninstall C:\RBuildTools and installed a fresh version off http://cran.r-project.org/bin/windows/Rtools/ ( installed version 3.5) into C:\Rtools. In installation I had the path variable option checked.
I reloaded RStudio and checked to make sure Rtools was found:
> devtools::find_rtools()
Error in system(full, intern = TRUE, ignore.stderr = quiet, ...) : running command '"C:/PROGRA~1/R/R-35~1.0/bin/x64/R" --no-site-file --no-environ --no-save --no-restore --quiet CMD config CC' had status 2
However, rtools appears in my PATH:
> Sys.getenv("PATH")
[1] "C:\\Program Files\\R\\R-3.5.0\\bin\\x64;C:\\Rtools\\bin;..."
So this doesn't appear to be an issue with Rtools not being added properly to my Path variable. Google searches have turned up seemingly related errors but nothing so far that solves my issue. I have tried both suggestions here and neither have worked. I wonder if this could be related to RStudio.
I had a similar problem with RTools 3.5.
The installer did add C:\RTools\bin to the PATH, but it did not add
C:\RTools\mingw_64\bin which apparently did cause some confusion.
After adding C:\RTools\mingw_64\bin to the PATH, everything was fine.
My symptoms were a bit different though: RStudio reported an error when trying to "Install and Restart" my package that RTools were not found, while devtools::find_rtools() reported them to be present.
I have a comprehensive answer here for rtools not being recognized thru use of pkgbuild
`devtools::install_github(repo)` keeps installing rtools35.exe
The code snippet acknowledges the github comment this is posted (helped by r-sig-finance citizens)
However, (I can't comment) the error of find_tools() has disappeared but remains in devtools::install_bitbucket() for the new code that was the ultimate target and is in a src/master on BB cloud.
I unloaded the devtools and installed with remotes
unloadNamespace("devtools")
library(remotes)
install_bitbucket(author/repo)
As I said the problem with find_tools is taken care of by pkgbuild loading all items
Try updating RStudio to the latest version.
I had this problem after updating Rtools to 3.5 and found that updating RStudio to 1.1.447 fixed it.
If that doesn't work, Can you run rstudioapi::versionInfo()$version from inside RStudio and share the output?
If this isn't your problem I found that RStudio keeps a log - and it helped me isolate this issue. In my case the file was located in, "C:\Users\my_windows_username\AppData\Local\RStudio-Desktop\log\rsession-my_windows_username.log"
I found this warning in the log time that corresponed to the error in RStudio
WARNING Unknown Rtools version: 3.5; LOGGED FROM: rstudio::core::Error rstudio::core::r_util::scanRegistryForRTools(HKEY, bool, std::vector*) C:\Users\Administrator\rstudio\src\cpp\core\r_util\RToolsInfo.cpp:269
This indicated that RStudio didn't recognize 3.5, which led me to check for an updated version of RStudio.
new to Cygwin. I downloaded apg-cyg and have been using it to install packages.
Recently I installed R and the current version in Cygwin packages is R.3.2.4. I wanted to install the latest R package but couldn't find a way from googling on how to do it inside Cygwin.
Is this possible to do or I just have to wait for the Cygwin packages updating their packages to the latest version? It would be nice to be able to update a package using the source file inside Cygwin..
Edit:
I should mention that I tried to install ggplot2 inside R using install.packages() and there was non-zero exit status and the installation couldn't go through.
You can install the source using cygwin setup. Click on the mouse on the "Src?" column.
The source will be installed in /usr/src
PS: next R release 3.3.1 is in 11 days. It will be packed for cygwin if there are no build issue
Followup:
There were several build issues, it took longer than expected to build 3.3.1
https://www.cygwin.com/ml/cygwin-announce/2016-06/msg00056.html
I was trying to install RTextTools package for R, but failed. Here is the output from the screen
> > install.packages("RTextTools")
Warning in install.packages("RTextTools") :
argument 'lib' is missing: using 'C:\Users\datamining\Documents/R/win-library/2.10'
--- Please select a CRAN mirror for use in this session ---
Warning: unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.10
Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
package ‘RTextTools’ is not available
What's the reason for this problem, and how to fix it? Thanks.
There are two distinct, but related, issues:
You are running version 2.10 of R which is two years old. CRAN supports only the current version with pre-built binaries. You could try installing from source.
RTextTools, as can be seen on its CRAN page also requires at least R version 2.13.
So in short: you should upgrade.
I have resolved the issue. I have Download RTextTools From Given Link.
https://cran.r-project.org/src/contrib/Archive/RTextTools/
and copy RTextTools_1.4.2.tar.gz file in project root folder then run this command in project folder in terminal
"R CMD INSTALL RTextTools_1.4.2.tar.gz"
After running this command I receive below error
"ERROR: dependencies ‘SparseM’, ‘randomForest’, ‘tree’, ‘e1071’, ‘ipred’, ‘caTools’, ‘maxent’, ‘glmnet’, ‘tau’ are not available for package ‘RTextTools’".
Now install each dependencies from RStudio or RConsole (Any Editor used by you) by simply running this code.
install.packages("caTools").
Install all 9 required packages One By One (In My Case it was 9 Packages Dependencies required by RTextTools) all packages will be installed except 'maxent'.
Now download maxent from the given link.
https://cran.r-project.org/src/contrib/Archive/maxent/.
and copy maxent_1.3.3.1.tar file in project folder then run this command in project folder in terminal.
"R CMD INSTALL maxent_1.3.3.1.tar"
Now For RTextTools Run this command again in Terminal.
"R CMD INSTALL RTextTools_1.4.2.tar.gz"
All is done Now..
But the Last Step is
Load the RTextTools using.
library(RTextTools)
You will see one more Error: Load SparseM Now Loading SparseM use code below.
library(SparseM)
and in the last Load RTextTools
library(RTextTools)
RTextTools is dependent on a number of packages, most of which require R 2.13+. You should always keep R updated to the latest version, since each update contains numerous bug fixes and performance enhancements.
If you can't install packages from repository or the packages are not available anymore, just follow this steps:
Install.packages("devtools")
check -- library("devtools")
install_github("cran/maxent")
install_github("cran/RTextTools")